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Hafeez A, Shabbir M, Khan K, Trembley JH, Badshah Y, Zafar S, Shahid K, Shah H, Ashraf NM, Hamid A, Afsar T, Almajwal A, Marium A, Razak S. Possible prognostic impact of PKCι genetic variants in prostate cancer. Cancer Cell Int 2024; 24:24. [PMID: 38200472 PMCID: PMC10782671 DOI: 10.1186/s12935-023-03182-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) have been linked with prostate cancer (PCa) and have shown potential as prognostic markers for advanced stages. Loss of function mutations in PKCι have been linked with increased risk of malignancy by enhancing tumor cell motility and invasion. We have evaluated the impact of two coding region SNPs on the PKCι gene (PRKCI) and their prognostic potential. METHODS Genotypic association of non-synonymous PKCι SNPs rs1197750201 and rs1199520604 with PCa was determined through tetra-ARMS PCR. PKCι was docked with interacting partner Par-6 to determine the effect of these variants on PKCι binding capabilities. Molecular dynamic simulations of PKCι docked with Par-6 were performed to determine variant effects on PKCι protein interactions. The possible impact of changes in PKCι protein interactions on epithelial cell polarity was hypothesized. RESULTS PKCι rs1199520604 mutant genotype TT showed association with PCa (p = 0.0055), while rs1197750201 mutant genotype AA also showed significant association with PCa (P = 0.0006). The binding interaction of PKCι with Par-6 was altered for both variants, with changes in Van der Waals energy and electrostatic energy of docked structures. CONCLUSION Genotypic analysis of two non-synonymous PKCι variants in association with PCa prognosis was performed. Both variants in the PB1 domain showed potential as a prognostic marker for PCa. In silico analysis of the effect of the variants on PKCι protein interactions indicated they may be involved in PCa progression through aberration of epithelial cell polarity pathways.
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Affiliation(s)
- Amna Hafeez
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan
| | - Maria Shabbir
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan.
| | - Khushbukhat Khan
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan
| | - Janeen H Trembley
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Minneapolis VA Health Care System Research Service, Minneapolis, MN, USA
| | - Yasmin Badshah
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan
| | - Sameen Zafar
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan
| | - Kanza Shahid
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan
| | - Hania Shah
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan
| | - Naeem Mahmood Ashraf
- Department of Biochemistry and Biotechnology, University of Gujrat, Hafiz Hayat Campus, Gujrat, 50700, Punjab, Pakistan
| | - Arslan Hamid
- University of Bonn, LIMES Institute (AG-Netea), Carl-Troll-Str. 31, 53115, Bonn, Germany
| | - Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ali Almajwal
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Afifa Marium
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia.
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Farajzadeh-Dehkordi M, Mafakher L, Harifi A, Haghdoost-Yazdi H, Piri H, Rahmani B. Unraveling the function and structure impact of deleterious missense SNPs in the human OX1R receptor by computational analysis. Sci Rep 2024; 14:833. [PMID: 38191899 PMCID: PMC10774445 DOI: 10.1038/s41598-023-49809-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/12/2023] [Indexed: 01/10/2024] Open
Abstract
The orexin/hypocretin receptor type 1 (OX1R) plays a crucial role in regulating various physiological functions, especially feeding behavior, addiction, and reward. Genetic variations in the OX1R have been associated with several neurological disorders. In this study, we utilized a combination of sequence and structure-based computational tools to identify the most deleterious missense single nucleotide polymorphisms (SNPs) in the OX1R gene. Our findings revealed four highly conserved and structurally destabilizing missense SNPs, namely R144C, I148N, S172W, and A297D, located in the GTP-binding domain. Molecular dynamics simulations analysis demonstrated that all four most detrimental mutant proteins altered the overall structural flexibility and dynamics of OX1R protein, resulting in significant changes in the structural organization and motion of the protein. These findings provide valuable insights into the impact of missense SNPs on OX1R function loss and their potential contribution to the development of neurological disorders, thereby guiding future research in this field.
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Affiliation(s)
- Mahvash Farajzadeh-Dehkordi
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran
- Department of Molecular Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Ladan Mafakher
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Abbas Harifi
- Department of Electrical and Computer Engineering, University of Hormozgan, Bandar Abbas, Hormozgan, Iran
| | - Hashem Haghdoost-Yazdi
- Cellular and Molecular Research Center, Research Institute for Prevention of Non-Communicable Disease, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Hossein Piri
- Cellular and Molecular Research Center, Research Institute for Prevention of Non-Communicable Disease, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Babak Rahmani
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran.
- Department of Molecular Medicine, Qazvin University of Medical Sciences, Qazvin, Iran.
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